Home  ›  The Role of Mirnas in Male Human Reproduction a Systematic Review

The Role of Mirnas in Male Human Reproduction a Systematic Review

Written By Sunday, April 17, 2022 Add Comment Edit
  • Research
  • Open Access
  • Published:

Hsa-mir-548 family expression in human being reproductive tissues

  • Birgitta Kaselti,
  • Maria Liivrand1,
  • Olli-Pekka Smolander1,
  • Andres Salumets2,3,4,five &
  • Agne Velthut-Meikas1

BMC Genomic Data book 22, Article number:xl (2021) Cite this commodity

Abstruse

Background

Hsa-miR-548ba expressed in ovarian granulosa cells targets PTEN and LIFR, which are essential for ovarian follicle activation and growth. The expression pattern of hsa-miR-548ba correlates with its host gene follicle-stimulating hormone receptor (FSHR), and FSH has a positive influence on hsa-miR-548ba expression. All the same, hsa-miR-548ba is a member of a big hsa-mir-548 family with potentially overlapping targets. The current study aims to investigate the co-expression of hsa-mir-548 family unit members in FSHR-positive reproductive tissues and to explore the potential co-regulation of pathways.

Results

For the higher up-described analysis, small RNA sequencing information from public data repositories were used. Sequencing results revealed that hsa-miR-548ba was expressed at the highest level in the ovarian granulosa cells and uterine myometrial samples together with another twelve and ane hsa-miR-548 family members, respectively. Pathway enrichment analysis of microRNA targets in the ovarian samples revealed the hsa-miR-548ba and hsa-miR-548b-5p co-regulation of RAB geranylgeranylation in mural granulosa cells. Moreover, other hsa-mir-548 family unit members co-regulate pathways essential for ovarian functions (PIP3 activates AKT signalling and signalling by ERBB4). In addition to hsa-miR-548ba, hsa-miR-548o-3p is expressed in the myometrium, which separately targets the peroxisome proliferator-activated receptor alpha (PPARA) pathway.

Conclusion

This study reveals that hsa-mir-548 family members are expressed in variable combinations in the reproductive tract, where they potentially fulfil dissimilar regulatory roles. The results provide a reference for further studies of the hsa-mir-548 family role in the reproductive tract.

Peer Review reports

Background

MicroRNAs (miRNAs) are a class of not-coding RNA molecules ~ 22 nucleotides in length with an important role in post-transcriptional gene expression regulation [1]. miRNAs target genes via the Watson-Crick complementarity principle. The seed sequences of miRNAs, the 2–7 nucleotides positioned in the 5′ region, play an important role in the precise targeting of mRNA [2, 3], while other regions in the miRNA sequence complement the target's specificity [4]. Overall, miRNAs play well-established roles in cistron expression regulation in normal and pathological weather condition [5]. Moreover, different tissues demonstrate variable miRNA expression patterns that determine tissue characteristics, differentiation, and functions [six].

miRNAs are categorized into families co-ordinate to the mature miRNA sequence and/or structure of their pre-miRNAs [7]. Mir-548 family unit miRNAs originate from the mariner-derived chemical element ane (Made1) transposable elements [8]: primate-specific short miniature inverted-repeat transposable elements (MITEs) that grade almost perfect palindromes. The secondary structure of Made1 RNA contains highly stable hairpin loops that are recognized by the miRNA-processing machinery [8]. Over the form of evolution, mir-548 family members have undergone several seed-shifting events, leading to changes in the seed sequences and hence the increased variability of their mRNA targets [9].

Human miRNA hsa-miR-548ba is a fellow member of the mir-548 family unit and was originally described in granulosa cells of man pre-ovulatory follicles. The hsa-miR-548ba gene is located in the intronic region of the follicle-stimulating hormone receptor (FSHR) factor [10]. Hsa-miR-548ba target assay has revealed PTEN and LIFR as its specific targets. Both of these genes play a well-established part in follicle activation and growth, indicating that hsa-miR-548ba may too take potential regulatory importance in follicle development [11].

Follicles are ovarian structures containing the oocyte and the supporting somatic cells: theca and granulosa cells, responsible for steroidogenesis and the metabolic support of the oocyte [12]. FSHR has important functions in follicle growth in the ovaries also as sperm development in the testes [13]. By the time the follicle reaches the pre-ovulatory stage, granulosa cells have differentiated into cumulus and landscape granulosa cell populations (CGC and MGC, respectively), and the follicle is filled with follicular fluid (FF) that physically separates these cell populations [12]. The main roles of CGC and MGC are providing essential metabolic support to the oocyte and steroid hormone production, respectively [12]. FSHR knock-out mice displayed disordered follicle growth and ovulation [14]. Similarly, point mutations in human FSHR outcome in arrested follicle development [15]. Therefore, disturbances in FSHR expression lead to female infertility [xiv, fifteen]. Analogously, Sertoli cells in the testes limited FSHR, where FSH binding indirectly activates the proliferation of germ lineage cells. FSH also regulates the role of Sertoli cells every bit supporters of sperm cell development [16]. Male person FSHR knock-out mice and humans with signal mutations in the FSHR gene have decreased spermatogenesis rates and are subfertile [17].

In addition to the ovary and testis, FSHR expression is also detected in the following reproductive tissues: the endometrium [18] and myometrium [19] of the uterus, fallopian tube [xx], and cervix [19]. The uterus is mainly composed of myometrial cells, the central roles of which are protecting the growing foetus and facilitating its delivery at the terminate of the pregnancy through muscular contractions [21, 22]. Myometrial smooth muscle cells express receptors for estrogen and progesterone important for myometrial jail cell growth and tissue activation during labour [21]. In improver, FSHR is present in the myometrium, where it may also participate in myometrial contractility [23]. The endometrium is a hormonally regulated inner lining of the uterus that is receptive for embryo implantation during just a short period of the menstrual cycle. During this period, the tissue develops specific functional and structural characteristics that allow the attachment of the embryo and its implantation [24, 25].

The aim of the current study is to empathize the gene regulatory network between hsa-mir-548 family members that are co-expressed in a certain cell blazon or tissue. Distinguishing their unique and overlapping factor targets will allow a meliorate interpretation of their importance in tissue function. Due to the importance of FSHR in folliculogenesis and the high level of expression of hsa-miR-548ba in granulosa cells, nosotros aimed to investigate the expression of all hsa-mir-548 members in the context of reproductive tissues where FSHR expression has been detected. We start by providing an update to the status of the hsa-mir-548 family according to the latest miRBase version [26]. Finally, we provide a model of potential co-regulation of mRNA targets and pathways between hsa-miR-548ba and other hsa-mir-548 family unit members in human being reproductive tissues.

The mir-548 family is primate-specific. Members of this family unit are plant in Human being sapiens, Pan troglodytes, Callithrix jacchus, Macaca mulatta, Pongo pygmaeus and Gorilla gorilla. MiR-548ba has been reported uniquely in Human sapiens; therefore, this study focuses but on the members detected in humans and excludes all other primates.

Results

According to the full version history of miRBase, the showtime members of the hsa-mir-548 family were added into v9. The number of members has since been increasing with almost all new releases of miRBase in correlation with the detection of new miRNA sequences due to the increasing availability of RNA sequencing data. MiRBase v22.1 contains 86 mature human mir-548 family sequences (Fig. 1A). Hsa-miR-548ba is a relatively new member of the family, added into v20.

Fig. 1
figure 1

Hsa-mir-548 family unit members in the miRBase database and in the human genome. (A) The number of all annotated human miRNA (grey line) and hsa-mir-548 family unit (black line) sequences in the full versions of the miRBase database. (B and C) Hsa-mir-548 family pre-miRNA sequences in the human genome: distribution by chromosome (B), distribution between the genomic loci (C)

Full size epitome

Human mir-548 family unit distribution throughout the human genome

The homo mir-548 family unit contains several multi-copy pre-miRNAs in the genome, and as a result, different miRNA precursor sequences requite rise to the aforementioned mature sequences of hsa-miR-548. For example, hsa-miR-548f and hsa-miR-548h take 5 different pre-miRNAs in the human genome. There are in total 76 different hsa-mir-548 pre-miRNA sequences, located throughout the man genome (Fig. 1B). The highest enrichment is observed on chromosomes 6, 8, and X. Two human chromosomes (19 and Y) lack hsa-mir-548 family sequences completely.

From the 76 hsa-mir-548 sequences, 54 are located in the intronic regions and 22 sequences are of intergenic origin (Fig. 1C). From 54 intronic miRNAs, 40 sequences were located on the same DNA strand as their host gene (Additional file 1 Supplementary Table S1). As 37 of these forty are protein-coding genes, there is a potential co-transcription of the host gene and the corresponding intronic miRNA.

Sequence similarity analysis of hsa-mir-548 family members

Sequence similarity analyses were performed for both mature and pre-miRNA sequences. Shorter distances between mature sequences on the phylogenetic tree signal higher conservation compared to pre-miRNA sequences (Additional file 2 Supplementary Fig. S1 and S2). The hsa-miR-548ba mature sequence displayed the shortest distances to the following miRNAs: hsa-miR-548 m, hsa-miR-548ag, hsa-miR-548d-5p, hsa-miR-548ay-5p, and hsa-miR-548ad-5p (Fig. 2C, Boosted file 2 Supplementary Fig. S1). In improver, hsa-miR-548ag; hsa-miR-548ai and hsa-miR-570-5p share the critical seed sequence with hsa-miR-548ba (Fig. second), although the two latter miRNAs demonstrate dissimilarities in their 3'part and therefore reside more distantly in the phylogenetic tree (Additional file 2 Supplementary Fig. S1).

Fig. 2
figure 2

The expression and sequence similarity of hsa-mir-548 family unit members in reproductive tissue samples. (A) The average number of hsa-mir-548 family members present in reproductive tissues with cut-off > 10 counts per meg (CPM). (B) The expression levels of hsa-miR-548ba in reproductive tissues. The sequencing results are displayed as a mean of CPM ± SEM. CGC–cumulus granulosa cells (n = 3), MGC–landscape granulosa cells (north = 3), testis (n = 5), SF–seminal fluid (n = i), pre-receptive endometrium (north = 12), receptive endometrium (n = 12), myometrium (n = 3), and cervix (n = four). (C) The closest hsa-mir-548 family members to hsa-miR-548ba co-ordinate to sequence similarity. (D) Hsa-mir-548 family members which share a seed sequence with hsa-miR-548ba. The sequence length in nucleotides is noted afterwards the slash. (Due east) miRNAs from the hsa-miR-548 family expressed in the myometrium. (F) miRNAs of the hsa-miR-548 family expressed in cumulus and mural granulosa cells. The alignment of hsa-miR-548 family sequences co-expressed with hsa-miR-548ba in the analysed tissues: (K) cumulus granulosa cells; (H) mural granulosa cells; (I) myometrium; (J) The expression of hsa-mir-548 family unit members in the cell-depleted follicular fluid of the ovarian follicle; (K) the alignment of extracellular miRNAs observed in follicular fluid. Expression levels are displayed every bit a mean of counts per million (CPM) ± SEM). *p < 0.05, Student's t-examination

Total size image

Moreover, a sequence similarity analysis was performed between hsa-mir-548 family members and Made1, the MITE elements giving ascension to these miRNAs (Boosted file two Supplementary Fig. S3 and S4, respectively). Hsa-miR-548-5p sequences demonstrate higher conservation and similarity to Made1 compared to hsa-miR-548-3p sequences. This result confirms a previous similar observation [nine]. Hsa-miR-548ba belongs to the hsa-miR-548-5p sequences and is therefore a more conserved family member. Hence, it is highly probable that hsa-miR-548ba and other hsa-mir-548 family members co-expressed in a tissue regulate a set of the same mRNA targets.

Hsa-mir-548 family expression in reproductive tissues

In society to quantify the expression levels of the hsa-miR-548 family members in human being reproductive tissues, small RNA high-throughput sequencing results from male and female reproductive tissues were analysed (Table one). Tissues were selected for assay co-ordinate to the availability of small RNA sequencing data and positivity for FSHR expression. From the male reproductive tissues, pocket-size RNA sequencing results were only available for the whole testis tissue homogenate and seminal fluid (SF). From the female reproductive tissues, data was available for MGC, CGC, and FF of the ovary, myometrium, and endometrium from the uterus and cervix.

Table 1 A clarification of data used in the hsa-mir-548 family analysis of reproductive tissues

Total size table

The highest number of hsa-mir-548 family members was detected from the SF, CGC, and MGC samples (cut-off > 10 counts per million (CPM), Fig. 2A). From the testis samples, none of the hsa-mir-548 family members reached the set cut-off limit (Fig. 2A). The total lists of hsa-mir-548 family members expressed above > 10 CPM cut-off level are presented in Additional file 1 Supplementary Table S2.

The highest expression levels of hsa-miR-548ba were observed in ovarian CGC and MGC samples (Fig. 2B). Outside of the ovary, hsa-miR-548ba expression was the highest in myometrial tissue compared to the other samples. Testicular, SF, endometrial, and cervical samples demonstrated expression levels with borderline detection values (Fig. 2B).

Hsa-mir-548 expression in granulosa cells and myometrium

To further report the potential and significance of the mail service-transcriptional co-regulation effect that hsa-miR-548ba may exhibit with its co-expressed family members, ovarian and myometrial samples were further analysed, as hsa-miR-548ba was only detected in these samples.

Sequencing results of granulosa cells revealed the expression of 13 unlike mature hsa-mir-548 family unit members (Fig. 2F). From those miRNAs, three (hsa-miR-548ab, hsa-miR-548ad-5p/ae-5p and hsa-miR-548ay) were differentially expressed between MGC and CGC samples (p < 0.05).

The miRNAs which share the aforementioned seed sequence with hsa-miR-548ba (Fig. 2D) are not co-expressed in granulosa cells. However, sequence alignment results reveal that a number of miRNAs detected in granulosa cells share the seed sequence with each other (Fig. 2G-H). Specifically, hsa-miR-548ab, hsa-miR-548d-5p, hsa-miR-548 h-5p, hsa-miR-548i, and hsa-miR-548w in CGC and hsa-miR-548ay, hsa-miR-548ae-5p, hsa-miR-548ad-5p, hsa-miR-548b-5p, hsa-miR-548d-5p and hsa-miR-548i in MGC contain the aforementioned seed sequences. Therefore, the co-regulation of common target genes by these miRNAs is possible and expected to occur in granulosa cells.

From miRNAs with the highest sequence similarity to hsa-miR-548ba, just hsa-miR-548ay-5p and hsa-miR-548ad-5p are present in MGC, and hsa-miR-548d-5p in both CGC and MGC are expressed above the cutting-off > 10 CPM (Fig. 2F-H).

Compared to granulosa cells, the myometrium expresses only two hsa-mir-548 family members in a higher place the > 10 CPM cut-off: hsa-miR-548ba and hsa-miR-548o-3p (Fig. 2E). Hsa-miR-548o-3p is evolutionarily distant from hsa-miR-548ba, and these 2 miRNAs do not share a mutual seed sequence (Fig. 2I). In addition to the myometrium, hsa-miR-548o-3p is expressed in the endometrium, cervix, and SF samples (Additional file one Supplementary Table S2).

Extracellular hsa-mir-548 family unit miRNAs in the follicular fluid

miRNAs are known to exist present in the extracellular space equally a role of RNA-bounden protein (RBP) complexes or as loaded into extracellular vesicles (EV) [33]. However, the potential for the hsa-mir-548 family unit miRNAs to exist secreted into extracellular spaces has not been studied. Due to the loftier expression levels of hsa-miR-548ba and several other members of the family unit in the ovarian follicular somatic cells, the extracellular profile was determined from the instance of the ovarian cell-depleted FF [22], where vii family members were detected (50% of samples > 10 CPM cutting-off, Fig. 2J). We observed that the miRNAs expressed at the highest levels in the cellular samples (hsa-miR-548k, hsa-miR-548ba and hsa-miR-548i) were not detected in FF. This suggests that those miRNAs are prison cell-specific and are not secreted into extracellular spaces. On the other mitt, hsa-miR-548o-5p, hsa-miR-548c-5p, hsa-miR-548am-5p, and hsa-miR-548b-3p in FF are not expressed in granulosa cells above the determined cut-off level (Fig. 2J).

Specific motifs in the iii′ half of the miRNA sequence have the potential to decide whether miRNAs are secreted into the extracellular space or are retained in the cells: for example, GGAG and UGCA appear frequently in extracellular and cellular miRNAs, respectively [34]. In improver, the AGG motif may be involved in extracellular miRNA trafficking [35]. All the same, miRNAs nowadays in FF samples do not comprise GGAG nor AGG motifs (Fig. 2K). Cellular motif UGCA is present in hsa-miR-548 h-3p/z. The fact that those miRNAs are present in the extracellular space may be the result of not-specific secretion.

The signature of hsa-mir-548 family unit expression is characteristic for each female reproductive tissue

All ovarian follicle sample types form separate clusters according to their hsa-mir-548 family expression patterns (Fig. 3A-B). Every bit expected, cellular and extracellular samples cluster separately. Moreover, 2 granulosa cell types class split clusters according to their hsa-mir-548 expression patterns (Fig. 3B). MGC and FF samples display more than like expression patterns compared to CGC cells (Fig. 3A-B). This may indicate that MGC is the main source of hsa-mir-548 members secreted into FF as MGC is the near abundant somatic cell type within the pre-ovulatory follicle.

Fig. 3
figure 3

Expression levels of hsa-mir-548 family miRNAs in the human ovarian follicle and uterine samples. (A) A heatmap of hsa-mir-548 family expression levels in individual ovarian samples; (B) a PCA plot of ovarian follicle cellular and extracellular samples according to the expression levels of hsa-mir-548 family miRNAs; (C) a heatmap of hsa-mir-548 family unit expression levels in private uterine samples; (D) a PCA plot of uterine samples according to the expression levels of hsa-mir-548 family levels. FF–cell-depleted follicular fluid, CGC–cumulus granulosa cells, MGC–mural granulosa cells. The location of hsa-miR-548ba on the heatmap is highlighted in red. The heatmap colour scale displays ln(x + 1) transformed CPM values

Full size image

In addition to granulosa cells, hsa-miR-548ba exhibited high expression levels in the myometrial tissue. For clustering assay, all available uterine tissue samples (endometrium, myometrium and cervix) were compared. The results exhibited a feature hsa-mir-548 family expression pattern for endometrium, myometrium, and cervical samples (Fig. 3C-D). Endometrial samples of pre-receptive and receptive stages clustered together (Fig. 3C-D), indicating that hsa-mir-548 family expression levels exercise non significantly change upon acquiring endometrial receptivity. Moreover, myometrial and cervical samples form closer clusters compared to endometrial samples (Fig. 3C).

Overall, the clustering assay illustrates that it is possible to distinguish female reproductive tissues and cell types by the expression signature of the hsa-mir-548 family members. Therefore, this miRNA family possesses regulatory roles specific to jail cell blazon.

Pathways regulated past hsa-miR-548 members co-expressed in granulosa cells

Since multiple hsa-mir-548 family members are co-expressed with hsa-miR-548ba in the ovarian granulosa cells, nosotros investigated their tissue-specific potential for regulating mutual signalling pathways with relevance to female fertility. Target genes were predicted for all miRNAs expressed above > 10 CPM cut-off level in CGC or MGC cells and the obtained lists were used equally inputs for Reactome pathway enrichment assay, the results of which are presented in Boosted file 1 Supplementary Tabular array S3. Target prediction results revealed that, despite the similarities between the sequences, miRNAs expressed in CGC or MGC target by and large individual genes with a small-scale overlapping function (Fig. 4A and B, respectively).

Fig. four
figure 4

Target prediction for hsa-mir-548 family miRNAs expressed in cumulus granulosa cells (A) and mural granulosa cells (B). Each orangish node represents 1 target gene, and genes targeted by more than one miRNA are connected with an edge

Full size prototype

Pathway enrichment assay of targeted genes ended that hsa-miR-548ba does non co-regulate mutual pathways in CGC with other cell-blazon-specific hsa-miR-548 family members. In MGC, hsa-miR-548ba revealed the co-regulation of "RAB geranylgeranylation" pathway with hsa-miR-548b-5p. From the other hsa-mir-548 family members hsa-miR-548d-5p and hsa-miR-548i co-regulate, "PIP3 activates the AKT signalling" pathway in both CGC and MGC. This pathway is additionally targeted past hsa-miR-548w and hsa-miR-548b-5p in CGC and MGC, respectively. Additionally, "PI5P, PP2A, and IER3 regulate PI3K/AKT signalling" pathway is commonly regulated past hsa-miR-548d-5p and hsa-miR-548b-5p in MGC (Boosted file 1 Supplementary Table S3A and S3B).

In the context of ovarian function, the to a higher place-mentioned pathways "PIP3 activates AKT signalling" and "PI5P, PP2A and IER3 regulate PI3K/AKT signalling" have been previously studied [36,37,38]. In improver, the "Translocation of SLC2A4 (GLUT4) to the plasma membrane" targeted by hsa-mir-548ba in both CGC and MGC, as well every bit "Signalling by ERBB4" targeted by hsa-miR-548b-5p in MGC, demonstrate the importance of the respective miRNAs in ovarian functions [39, 40].

Pathways regulated by hsa-miR-548 members expressed in myometrium

Although the myometrial cells exhibited the expression of only two hsa-mir-548 family members (hsa-miR-548ba and hsa-miR-548o-3p), a commonly regulated pathway "Signalling past BRAF and RAF fusions" past these two miRNAs was detected.

In the context of myometrial functions, the following important regulatory pathways were targeted by hsa-miR-548o-3p: "PI5P, PP2A and IER3 regulate PI3K/AKT signalling" and "PPARA activates gene expression".

Discussion

Hsa-mir-548 is a primate-specific miRNA family unit derived from Made1 transposable chemical element [8]. Made1 elements are MITEs with genomic locations either close to or within genes, where they may exist involved in cistron regulation [41]. Hsa-mir-548 family members are transcribed from most human being chromosomes, while some other miRNA families exhibit chromosome-specific locations in the genome [vii]. The distribution analysis of hsa-mir-548 family members in the homo genome exhibited that the bulk of pre-miRNA sequences (54/76) are located in the intronic regions of genes. This is in an accordance with the preferable genome locations of MITEs [41]. Moreover, chromosome Y, which contains the smallest number of genes compared to other chromosomes [42], does not contain whatsoever hsa-mir-548 members. However, cistron-rich chromosome 19 [43] likewise did not contain any hsa-mir-548 miRNA sequences. It is possible that not all hsa-mir-548 family members take been discovered. Since the offset sequence of hsa-mir-548 was included to miRBase, new sequences accept been added to nigh every new miRBase release, correlating with the rapid development and reduced toll of high-throughput sequencing technologies. Moreover, using a bioinformatic arroyo, 34 boosted precursor sequences of hsa-mir-548 take been discovered, indicating that this family could be larger [44]. However, their expression all the same needs experimental validation.

miRNAs are important gene expression regulators in both the male person and female reproductive tissues and aberrant miRNA expression tin can atomic number 82 to infertility [45, 46]. Hsa-miR-548ba expression analysis in reproductive samples revealed that this particular miRNA is expressed at the highest level in granulosa cells, where information technology was first discovered. Information technology has been previously shown that the expression pattern of hsa-miR-548ba is similar to that of FSHR and FSH treatment upregulates hsa-miR-548ba expression levels in human being granulosa cells [11]. Human ovarian granulosa cells [13], endometrium [47], myometrium [19], cervix [19] and testis Sertoli cells [13] all express FSHR. In addition to granulosa cells, hsa-miR-548ba exhibited high expression levels in the myometrial tissue. These results reveal the tissue-specific expression of hsa-miR-548ba that may be derived from a unlike miRNA expression regulation than that observed in the granulosa cells of its host factor, FSHR. However, differences in expression level may likewise be caused by technical errors. The datasets used for this report were obtained from information repositories and, therefore, RNA extraction and library training were non universal for all samples. This may be the crusade of the lower expression of hsa-miR-548ba in the endometrium, neck, and testis samples.

Overall, granulosa cells limited 13 members of the hsa-mir-548 family. From those, miRNAs hsa-miR-548ab, hsa-miR-548ad-5p/ae-5p, and hsa-miR-548ay-5p were differentially expressed between MGC and CGC samples (p-value < 0.05). Although detected in a few other human being sample types (hsa-miR-548ab expression is reported in human B-cells [48], hsa-miR-548ad-5p/ae-5p and hsa-miR-548ay-5p are nowadays in synovial tissue samples [49], and hsa-miR-548ad-5p is present in claret plasma samples), the roles of these specific miRNAs accept non been investigated. Yet, in our samples, hsa-miR-548ad-5p was detected in extracellular FF as i of the most abundant miRNAs. According to the comparisons in ovarian datasets, it can be deduced that hsa-miR-548ad-5p is secreted from MGC and may be involved in intercellular signalling in the follicle. Therefore, the investigated miRNA family potentially has unknown importance in follicular function.

miRNAs which share the same seed sequence with hsa-miR-548ba are not co-expressed in granulosa cells, which indicates that this miRNA potentially has an individual specific regulatory role in the ovary. Yet, despite this, some targets were shared between other co-expressed members of the hsa-mir-548 family with different seed sequences. It has been well established that one mRNA can be targeted by multiple miRNAs [50]. Moreover, target prediction algorithms like miRWalk apply additional features to miRNA seed sequence for target prediction [51]. The hsa-mir-548 family has gone through several seed-shifting events, which has resulted in various seed sequences in the members [nine]. Different seed sequence variants were also present in miRNAs expressed in ovarian and myometrial samples. Still, some hsa-mir-548 family miRNAs expressed in granulosa cells take common seed sequences and consequently overlap with office of the predicted target genes; for example, hsa-miR-548b-5p, hsa-miR-548d-5p, and hsa-miR-548i expressed in MGCs.

The majority of enriched pathways were targeted by dissimilar private miRNAs in the granulosa cells. All together there were 3 exceptions. The first exception was the "PIP3 activates AKT signaling" pathway, which is targeted past hsa-miR-548d-5p and hsa-miR-548i in CGC and MGC and additionally targeted by hsa-miR-548w and hsa-miR-548b-5p in CGC and MGC, respectively. This pathway is involved in regulating the balance betwixt dormancy and activation of follicles, granulosa jail cell differentiation, and proliferation [38]. The second exception was the "PI5P, PP2A, and IER3 regulate PI3K/AKT signalling" pathway targeted by hsa-miR-548d-5p in CGC and MGC, and hsa-miR-548b-5p in MGC. IER3 is a part of a gonadotropin-EGR2-IER3 axis with a office in granulosa jail cell survival during follicle evolution [36]. Additionally, PP2A participates in the regulation of PKC-mediated inflammation in rat granulosa cells [37]. The last co-regulated pathway is "RAB geranylgeranylation" targeted by hsa-miR-548ba and hsa-miR-548b-5p in MGC. The depletion of the geranylgeranylation substrate geranylgeranyl diphosphate (GGPP) in mice oocytes inhibits Rab27a geranylgeranylation, which is required for Rab protein activation. Rab27a plays a possible role in oocyte protein secretion. Therefore, disturbances in this pathway impair oocyte-granulosa cell communication, which is necessary for normal follicle development [52].

Pathways targeted by private hsa-mir-548 members accept boosted known roles in granulosa cells. For instance, hsa-miR-548ba targets the "translocation of SLC2A4 (GLUT4) to the plasma membrane" pathway. GLUT4 is involved in glycose uptake and FSH stimulates this process in granulosa cells [39]. Granulosa cells of polycystic ovarian syndrome patients have a tendency to brandish abnormal glycose metabolism. Therefore, normal glycose metabolism is important for granulosa cell function [39]. Hsa-miR-548b-5p targets "Signalling past ERBB4" in MGC. ERBB4 plays a role in normal follicle development and disturbances in ERBB4 levels may lead to ovarian dysfunction [40]. To conclude, in addition to hsa-miR-548ba, other hsa-mir-548 family members regulate pathways important for granulosa cell functions.

Pathways "PIP3 activates AKT signalling" and "PI5P, PP2A and IER3 Regulate PI3K/AKT signalling" are targeted by miRNAs which share the seed sequences (hsa-miR-548d-5p, hsa-miR-548b-5p, hsa-miR-548i, and hsa-miR-548w). Nonetheless, boosted family members expressed in granulosa cells have the same seed sequence but do non target those pathways. Alignment results of miRNAs present in granulosa cells and alignment of the whole miRNA family unit demonstrated that, in addition to seed shifting events, nucleotide substitutions are present in miRNA sequences. These molecular events accept changed potential targeting features [4] and accept led to different target genes between miRNAs with the same seed sequence.

Myometrial samples limited two hsa-mir-548 members: hsa-miR-548ba and hsa-miR-548o-3p. Both miRNAs regulate 1 common pathway: "Signalling by BRAF and RAF fusions". BRAF and RAF fusion is a result of chromosomal rearrangement events and is detected in singled-out cancer types [53]. Therefore, in normal myometrial tissue, this pathway is not present. In improver, hsa-miR-548o-3p targets the "PI5P, PP2A, and IER3 regulate PI3K/AKT signalling" and "PPARA activates gene expression" pathways. From the beginning targeted pathway, PP2A regulates proteins involved in smooth muscle contraction [54]. In the 2d pathway, PPARA levels increase in the belatedly pregnancy myometrium (gestation range 20–35 weeks) compared to nonpregnant women and decrease by the time of labour, suggesting that PPARA plays a role in maintaining pregnancy [55]. This indicates that the hsa-mir-548 family may have a regulatory role in myometrial gene expression regulation involved in contractile functions. Moreover, hsa-miR-548o-3p expression was non detected in ovarian samples but was present in endometrial and cervical samples, confirming its organ-specific expression.

miRNAs have been detected from all body fluids, including FF [32, 56], and may exist involved in cell-to-jail cell communication [33]. miRNAs tin can exist secreted from cells as a office of RBPs or packed into EVs [33]. Many possible sorting mechanisms are proposed for loading miRNAs into EVs: sequence characteristics, post-transcriptional modifications, subcellular location, and intracellular concentration [33]. In this report, FF which contains both RBPs and EVs, was searched for hsa-mir-548 family unit members. As a upshot, 7 miRNAs were detected in FF. Some of the miRNAs were simply detected in FF and not in granulosa cells, for instance, hsa-miR-548o-5p and hsa-miR-548c-5p. miRNAs expressed at the highest levels in cellular samples were not present in FF, indicating that the secretion mechanism is not based on the intercellular concentration of miRNA molecules. miRNAs nowadays in extracellular samples were aligned and a possible consign motif was searched for. Known miRNA secretion motifs GGAG [34] and AGG [35] are not nowadays in the miRNA sequences of hsa-mir-548 family members present in FF. Nevertheless, hsa-mir-548 family members take been detected from other trunk fluids in addition to FF: hsa-miR-548b-5p, hsa-miR-548c-5p and hsa-miR-548i [57], and hsa-miR-548a-3p [58] in blood serum samples, hsa-miR-548b-3p in blood plasma, bronchial lavage and peritoneal fluid, and hsa-miR-548d-5p in amniotic fluid [59]. Some miRNAs infiltrate into the FF from blood plasma [32], explaining the lack of their expression in the granulosa cells. Additionally, the oocyte has not been investigated as the source of miRNAs secreted into the FF due to the lack of such human data. Therefore, hsa-mir-548 family members are secreted into extracellular space by other prison cell types as well as ovarian granulosa cells. The machinery by which hsa-mir-548 family members are selected for secretion remains unknown.

Conclusion

From all the analysed FSHR-positive samples, hsa-miR-548ba transcribed from the intronic region of FSHR gene can be detected in the ovarian granulosa cells and the myometrium. This suggests that the expression of hsa-miR-548ba and FSHR are differently co-regulated in other FSHR-positive tissues. In improver to hsa-miR-548ba, twelve and ane other hsa-mir-548 family members are expressed in granulosa and myometrium samples, respectively. Moreover, hsa-mir-548 family members are detectable from the extracellular ovarian FF. miRNA target pathway enrichment analysis revealed that hsa-miR-548ba and hsa-miR-548b-5p co-regulate the RAB geranylgeranylation pathway in MGC. Disturbances in this pathway impair oocyte-granulosa cell communication. In addition to hsa-miR-548ba, other family members separately regulate essential pathways for granulosa cell part (PIP3 activates AKT signalling and signalling by ERBB4). This reveals that hsa-mir-548's family unit regulatory role in granulosa cells is wider than previously best-selling. Moreover, hsa-miR-548o-3p expressed in myometrium targets the PPARA pathway which is associated with the maintenance of pregnancy. Furthermore, hsa-miR-548o-3p presents uterine-specific expression as it was detected simply in myometrial, endometrial and cervical samples. Overall, hsa-mir-548 family members may play regulatory roles in ovarian follicle activation, evolution, granulosa cell differentiation, and proliferation. In the myometrium, the hsa-mir-548 family was predicted to regulate myometrial contractility and has a potential importance in the maintenance of pregnancy.

Methods

Hsa-mir-548 family members and sequences

The assay of hsa-mir-548 family member curation was performed using the miRBase database [26]. Information most miRNA mature sequences was downloaded from all full miRBase versions with the exception of v22.ane, which is the electric current release. Genomic locations of pre-miRNA sequences in the man genome were obtained from NCBI Gene [lx] and Ensembl [61] databases.

Mature and pre-miRNA sequences were aligned in Jalview (v2.xi.0) [62] using the Clustal Omega algorithm with standard settings [63]. Phylogenetic trees of mature and pre-miRNA sequences were constructed with the neighbour-joining method [64] from reads aligned with Clustal Omega in Jalview.

Hsa-mir-548 family unit expression in human reproductive tissues

All sequencing information used in the analyses were previously published and available in open up information repositories (Table 1). From all available data, but samples from healthy command subjects were used. All miRNA raw FASTQ files were quality-filtered with Trimmomatic v0.39 [65] with the options of SLIDINGWINDOW:2:20. Adapter sequences were removed and reads below 17 nucleotides in length were discarded. The remaining filtered and trimmed reads were counted and mapped to the main assembly of human genome GRCh38 and annotated miRNA sequences from miRBase v22.1 using miRDeep2 with standard settings [66]. All miRNA raw counts obtained from miRDeep2 results were normalized to counts per million (CPM) using the edgeR bundle v.3.28.1 [67]. miRNA results were filtered by expression levels, and the cut-off was set > 10 CPM for all cellular samples. The cut-off for extracellular samples was set to > 10 CPM in 50% of samples. Data visualization on heatmap and PCA plots was performed in ClustVis [68]. Statistical significance between CGC and MGC was calculated via a ii-tailed Student's t-exam. The statistical significance level was gear up at p < 0.05.

Target prediction and gene ontology analysis

Target genes were predicted for miRNAs with an expression cut-off level of > ten CPM with miRWalk version 3 [51]. Obtained miRNA target lists were input for cistron enrichment assay with miRWalk pathway analysis tool, and a statistical significance threshold was prepare at Benjamini-Hochberg FDR < 0.i.

Availability of data and materials

Abbreviations

CGC:

cumulus granulosa cells

CPM:

counts per million

EV:

extracellular vesicles

FF:

follicular fluid

FSHR:

follicle-stimulating hormone receptor

Made:

mariner-derived chemical element 1

MGC:

mural granulosa cells

MITEs:

miniature inverted-repeat transposable elements

RBP:

RNA-bounden protein

SF:

seminal fluid

References

  1. Bartel DP. MicroRNAs: genomics, biogenesis, machinery, and part. Cell. 2004 Jan 23;116(2):281–97. https://doi.org/10.1016/S0092-8674(04)00045-5.

    CAS  Commodity  PubMed  Google Scholar

  2. Lewis BP. Shih I -hung, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of Mammalian MicroRNA Targets Jail cell. 2003 December 26;115(7):787–98. https://doi.org/x.1016/s0092-8674(03)01018-three.

    CAS  Article  PubMed  Google Scholar

  3. Bartel DP. MicroRNA target recognition and regulatory functions. Cell. 2009 Jan 23;136(2):215–33. https://doi.org/10.1016/j.cell.2009.01.002.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  4. Ding J, Li Ten, Hu H. TarPmiR: a new approach for microRNA target site prediction. Bioinformatics. 2016 Sep 15;32(eighteen):2768–75. https://doi.org/10.1093/bioinformatics/btw318.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  5. Sereno Thou, Videira M, Wilhelm I, Krizbai IA, Brito MA. miRNAs in Health and Affliction: A Focus on the Chest Cancer Metastatic Cascade towards the Encephalon. Cells [Net]. 2020 Jul 28 [cited 2020 Dec 15];9(8). Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463742/

  6. Ludwig Northward, Leidinger P, Becker K, Backes C, Fehlmann T, Pallasch C, et al. Distribution of miRNA expression across human tissues. Nucleic Acids Res. 2016 May 5;44(8):3865–77. https://doi.org/10.1093/nar/gkw116.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  7. Kamanu TKK, Radovanovic A, Archer JAC, Bajic VB. Exploration of miRNA families for hypotheses generation. Sci Rep [Internet]. 2013 Oct 15 [cited 2020 Dec 15];iii. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3796740/

  8. Piriyapongsa J, Jordan IK. A Family unit of Man MicroRNA Genes from Miniature Inverted-Repeat Transposable Elements. PLoS One [Internet]. 2007 Feb 14 [cited 2020 Dec 15];2(2). Bachelor from: https://www.ncbi.nlm.nih.gov/pmc/manufactures/PMC1784062/

  9. Liang T, Guo L, Liu C. Genome-Broad Analysis of mir-548 Cistron Family Reveals Evolutionary and Functional Implications J Biomed Biotechnol [Internet]. 2012 [cited 2020 Dec xv];2012 Bachelor from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468316/

  10. Velthut-Meikas A, Simm J, Tuuri T, Tapanainen JS, Metsis 1000, Salumets A. Enquiry resource: small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes. Mol Endocrinol. 2013 Jul;27(vii):1128–41. https://doi.org/ten.1210/me.2013-1058.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  11. Rooda I, Hensen Thou, Kaselt B, Kasvandik S, Pook One thousand, Kurg A, et al. Target prediction and validation of microRNAs expressed from FSHR and aromatase genes in human being ovarian granulosa cells. Sci Rep. 2020 Feb 10;10(1):2300. https://doi.org/10.1038/s41598-020-59186-10.

    CAS  Article  PubMed  PubMed Primal  Google Scholar

  12. Hennet ML, Combelles CMH. The antral follicle: a microenvironment for oocyte differentiation. Int J Dev Biol. 2012;56(x–12):819–31. https://doi.org/10.1387/ijdb.120133cc.

    CAS  Article  PubMed  Google Scholar

  13. Simoni M, Gromoll J, Nieschlag East. The follicle-stimulating hormone receptor: biochemistry, molecular biology, physiology, and pathophysiology*. Endocr Rev. 1997 December one;18(half dozen):739–73. https://doi.org/10.1210/edrv.18.6.0320.

    CAS  Article  PubMed  Google Scholar

  14. Danilovich N, Babu PS, Xing W, Gerdes 1000, Krishnamurthy H, Sairam MR. Estrogen deficiency, obesity, and skeletal abnormalities in follicle-stimulating hormone receptor knockout (FORKO) female person mice**this investigation was supported in function by the Canadian Institutes of Health Inquiry. Endocrinology. 2000 Nov 1;141(xi):4295–308. https://doi.org/x.1210/endo.141.eleven.7765.

    CAS  Commodity  PubMed  Google Scholar

  15. Aittomäki K, Lucena JL, Pakarinen P, Sistonen P, Tapanainen J, Gromoll J, et al. Mutation in the follicle-stimulating hormone receptor gene causes hereditary hypergonadotropic ovarian failure. Cell. 1995 Sep 22;82(6):959–68. https://doi.org/10.1016/0092-8674(95)90275-9.

    Article  PubMed  Google Scholar

  16. Petersen C, Söder O. The Sertoli prison cell – a hormonal target and 'super' nurse for germ cells that determines testicular size. HRP. 2006;66(four):153–61. https://doi.org/10.1159/000094142.

    CAS  Article  Google Scholar

  17. Oduwole OO, Peltoketo H, Huhtaniemi IT. Role of Follicle-Stimulating Hormone in Spermatogenesis. Front end Endocrinol (Lausanne) [Net]. 2018 Dec 14 [cited 2021 January 7];9. Bachelor from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302021/

  18. Ponikwicka-Tyszko D, Chrusciel Thou, Stelmaszewska J, Bernaczyk P, Sztachelska M, Sidorkiewicz I, et al. Functional Expression of FSH receptor in Endometriotic lesions. The Journal of Clinical Endocrinology & Metabolism. 2016 Jul 1;101(7):2905–14. https://doi.org/10.1210/jc.2016-1014.

    CAS  Commodity  Google Scholar

  19. Stilley JAW, Christensen DE, Dahlem KB, Guan R, Santillan DA, England SK, et al. FSH receptor (FSHR) expression in human extragonadal reproductive tissues and the developing placenta, and the bear upon of its deletion on pregnancy in mice. Biol Reprod. 2014 Sep;91(3):74. https://doi.org/10.1095/biolreprod.114.118562.

    CAS  Commodity  PubMed  PubMed Central  Google Scholar

  20. Zheng W, Magid MS, Kramer EE, Chen YT. Follicle-stimulating hormone receptor is expressed in homo ovarian surface epithelium and fallopian tube. Am J Pathol. 1996 January;148(i):47–53.

    CAS  PubMed  PubMed Primal  Google Scholar

  21. Ono Yard, Bulun SE, Maruyama T. Tissue-Specific Stem Cells in the Myometrium and Tumor-Initiating Cells in Leiomyoma. Biol Reprod [Net]. 2014 Dec [cited 2021 Jan 25];91(6). Available from: https://www.ncbi.nlm.nih.gov/pmc/manufactures/PMC4434985/

  22. Shynlova O, Tsui P, Jaffer Southward, Lye SJ. Integration of endocrine and mechanical signals in the regulation of myometrial functions during pregnancy and labour. European Journal of Obstetrics & Gynecology and Reproductive Biological science. 2009 May 1;144:S2–10. https://doi.org/10.1016/j.ejogrb.2009.02.044.

    CAS  Article  Google Scholar

  23. Chrusciel M, Ponikwicka-Tyszko D, Wolczynski Due south, Huhtaniemi I, Rahman NA. Extragonadal FSHR Expression and Role—Is Information technology Real? Front end Endocrinol [Net]. 2019 [cited 2021 January 28];10. Bachelor from: https://www.frontiersin.org/articles/x.3389/fendo.2019.00032/full#B16

  24. Riesewijk A, Martín J, van Os R, Horcajadas JA, Polman J, Pellicer A, et al. Gene expression profiling of human endometrial receptivity on days LH+ii versus LH+7 by microarray engineering. Mol Hum Reprod. 2003 May ane;nine(5):253–64. https://doi.org/10.1093/molehr/gag037.

    CAS  Commodity  PubMed  Google Scholar

  25. Wang W, Vilella F, Alama P, Moreno I, Mignardi M, Isakova A, et al. Single-prison cell transcriptomic atlas of the human being endometrium during the menstrual cycle. Nat Med. 2020 October;26(10):1644–53. https://doi.org/10.1038/s41591-020-1040-z.

    CAS  Article  PubMed  Google Scholar

  26. Kozomara A, Birgaoanu M, Griffiths-Jones South. miRBase: from microRNA sequences to function. Nucleic Acids Res. 2019 January eight;47(D1):D155–62. https://doi.org/10.1093/nar/gky1141.

    CAS  Commodity  PubMed  Google Scholar

  27. Rekker K, Altmäe South, Suhorutshenko M, Peters One thousand, Martinez-Blanch JF, Codoñer FM, et al. A 2-Cohort RNA-seq Written report Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women. Genes (Basel) [Internet]. 2018 November 23 [cited 2020 Dec 20];9(12). Bachelor from: https://www.ncbi.nlm.nih.gov/pmc/manufactures/PMC6315937/

  28. Chuang T-D, Khorram O. Expression profiling of lncRNAs, miRNAs, and mRNAs and their differential Expression in leiomyoma using next-generation RNA sequencing. Reprod Sci. 2018 February;25(2):246–55. https://doi.org/ten.1177/1933719117711265.

    CAS  Article  PubMed  Google Scholar

  29. Xu J, Zou J, Wu L, Lu W. Transcriptome analysis uncovers the diagnostic value of miR-192-5p/HNF1A-AS1/VIL1 console in cervical adenocarcinoma. Sci Rep [Net]. 2020 Oct 6 [cited 2021 Jan thirteen];10. Bachelor from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7538942/

  30. An Integrated Encyclopedia of DNA Elements in the Man Genome. Nature. 2012 Sep 6;489(7414):57–74.

  31. Selth LA, Roberts MJ, Chow CWK, Marshall VR, Doi SAR, Vincent AD, et al. Human seminal fluid as a source of prostate cancer-specific microRNA biomarkers. Endocr Relat Cancer. 2014 Aug 1;21(4):L17–21. https://doi.org/x.1530/ERC-14-0234.

    CAS  Commodity  PubMed  Google Scholar

  32. Rooda I, Hasan MM, Roos One thousand, Viil J, Andronowska A, Smolander O-P, et al. Cellular, Extracellular and Extracellular Vesicular miRNA Profiles of Pre-Ovulatory Follicles Indicate Signaling Disturbances in Polycystic Ovaries. Int J Mol Sci. 2020 Dec;15, 21(24).

  33. Fritz JV, Heintz-Buschart A, Ghosal A, Wampach Fifty, Etheridge A, Galas D, et al. Sources and functions of extracellular small RNAs in man apportionment. Annu Rev Nutr. 2016 Jul 17;36(1):301–36. https://doi.org/x.1146/annurev-nutr-071715-050711.

    CAS  Commodity  PubMed  PubMed Central  Google Scholar

  34. Villarroya-Beltri C, Gutiérrez-Vázquez C, Sánchez-Cabo F, Pérez-Hernández D, Vázquez J, Martin-Cofreces N, et al. Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs. Nat Commun. 2013 Dec 20;iv(1):2980. https://doi.org/10.1038/ncomms3980.

    CAS  Article  PubMed  Google Scholar

  35. Lee H, Li C, Zhang Y, Zhang D, Otterbein LE, Jin Y. Caveolin-1 selectively regulates microRNA sorting into microvesicles after baneful stimuli. J Exp Med. 2019 Sep two;216(ix):2202–20. https://doi.org/ten.1084/jem.20182313.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  36. Jin H, Won Thou, Shin E, Kim H-M, Lee M, Bae J. EGR2 is a gonadotropin-induced survival factor that controls the expression of IER3 in ovarian granulosa cells. Biochem Biophys Res Commun. 2017 January 22;482(4):877–82. https://doi.org/10.1016/j.bbrc.2016.11.127.

    CAS  Article  PubMed  Google Scholar

  37. Lin Y-Y, Sun D, Wu Y-50. Novel regulation of PKC-induced inflammation by Akt and protein phosphatase 2A in ovarian granulosa cells. Chin J Physiol. 2020 Aug;63(4):179–86. https://doi.org/x.4103/CJP.CJP_44_20.

    CAS  Commodity  PubMed  Google Scholar

  38. Makker A, Goel MM, Mahdi AA. PI3K/PTEN/Akt and TSC/mTOR signaling pathways, ovarian dysfunction, and infertility: an update. J Mol Endocrinol. 2014 Dec 1;53(3):R103–18. https://doi.org/10.1530/JME-14-0220.

    CAS  Article  PubMed  Google Scholar

  39. Anjali G, Kaur South, Lakra R, Taneja J, Kalsey GS, Nagendra A, et al. FSH stimulates IRS-2 expression in human granulosa cells through cAMP/SP1, an inoperative FSH activeness in PCOS patients. Cell Signal. 2015 Dec 1;27(12):2452–66. https://doi.org/10.1016/j.cellsig.2015.09.011.

    CAS  Commodity  PubMed  Google Scholar

  40. Veikkolainen V, Ali Due north, Doroszko Thousand, Kiviniemi A, Miinalainen I, Ohlsson C, et al. Erbb4 regulates the oocyte microenvironment during folliculogenesis. Hum Mol Genet. 2020 Oct x;29(17):2813–xxx. https://doi.org/ten.1093/hmg/ddaa161.

    CAS  Article  PubMed  Google Scholar

  41. Fattash I, Rooke R, Wong A, Hui C, Luu T, Bhardwaj P, et al. Miniature inverted-repeat transposable elements: discovery, distribution, and activeness. Genome. 2013 Sep;56(nine):475–86. https://doi.org/10.1139/gen-2012-0174.

    CAS  Article  PubMed  Google Scholar

  42. Quintana-Murci 50, Fellous M. The human Y chromosome: the biological part of a "functional wasteland." J Biomed Biotechnol 2001;1(1):xviii–24, The Human being Y Chromosome: The Biological Role of a "Functional Wasteland", doi: https://doi.org/ten.1155/S1110724301000080.

  43. Tanabe H, Müller S, Neusser M, von Hase J, Calcagno Due east, Cremer M, et al. Evolutionary conservation of chromosome territory arrangements in cell nuclei from college primates. Proc Natl Acad Sci U S A. 2002 Apr ii;99(7):4424–9. https://doi.org/10.1073/pnas.072618599.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  44. Bell J, Larson K, Kutzler M, Bionaz Grand, Löhr CV, Hendrix D. miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs. PLOS Computational Biology. 2019 Sep ten;fifteen(ten):e1007309.

    CAS  Article  Google Scholar

  45. Salas-Huetos A, James ER, Aston KI, Carrell DT, Jenkins TG, Yeste Chiliad. The role of miRNAs in male person human reproduction: a systematic review. Andrology. 2020 Jan 1;8(i):7–26. https://doi.org/10.1111/andr.12714.

    CAS  Commodity  PubMed  Google Scholar

  46. Salas-Huetos A, James ER, Aston KI, Jenkins TG, Carrell DT, Yeste M. The Expression of miRNAs in human being ovaries, oocytes, extracellular vesicles, and early embryos: a systematic review. Cells. 2019 December;4(12):viii(12). https://doi.org/x.3390/cells8121564.

    CAS  Article  Google Scholar

  47. Sacchi Southward, Sena P, Degli Esposti C, Lui J, La Marca A. Show for expression and functionality of FSH and LH/hCG receptors in human endometrium. J Help Reprod Genet. 2018 Sep;35(nine):1703–12. https://doi.org/x.1007/s10815-018-1248-viii.

    Article  PubMed  PubMed Key  Google Scholar

  48. Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WWL, et al. Deep sequencing of the small RNA transcriptome of normal and cancerous human being B cells identifies hundreds of novel microRNAs. Blood. 2010 Dec 2;116(23):e118–27. https://doi.org/10.1182/claret-2010-05-285403.

    CAS  Article  PubMed  PubMed Key  Google Scholar

  49. Zhou Y, Wang Z, Chen 10, Zhang J, Yang L, Liu Due south, et al. Identification of differentially expressed miRNAs and mRNAs in synovial of osteoarthritis via RNA-sequencing. BMC Med Genet [Internet]. 2020 Mar ii [cited 2020 Dec 22];21. Available from: https://www.ncbi.nlm.nih.gov/pmc/manufactures/PMC7053084/

  50. Wu Due south, Huang Southward, Ding J, Zhao Y, Liang L, Liu T, et al. Multiple microRNAs modulate p21Cip1/Waf1 expression by straight targeting its three′ untranslated region. Oncogene. 2010 Apr 15;29(15):2302–8. https://doi.org/10.1038/onc.2010.34.

    CAS  Article  PubMed  Google Scholar

  51. Sticht C, De La Torre C, Parveen A, Gretz N. miRWalk: An online resources for prediction of microRNA binding sites. PLoS One. 2018;xiii(ten):e0206239.

    Article  Google Scholar

  52. Jiang C, Diao F, Sang Y-J, Xu N, Zhu R-L, Wang X-X, et al. GGPP-Mediated Protein Geranylgeranylation in Oocyte Is Essential for the Institution of Oocyte-Granulosa Cell Communication and Primary-Secondary Follicle Transition in Mouse Ovary. PLoS Genet [Internet]. 2017 Jan 10 [cited 2021 Jan 28];13(1). Bachelor from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224981/

  53. Lavoie H, Therrien Thou. Regulation of RAF protein kinases in ERK signalling. Nat Rev Mol Cell Biol. 2015 May;16(5):281–98. https://doi.org/10.1038/nrm3979.

    CAS  Article  PubMed  Google Scholar

  54. Butler T, Paul J, Europe-Finner N, Smith R, Chan E-C. Role of serine-threonine phosphoprotein phosphatases in smooth muscle contractility. Am J Phys Prison cell Phys. 2013 January sixteen;304(6):C485–504. https://doi.org/x.1152/ajpcell.00161.2012.

    CAS  Article  Google Scholar

  55. Dong K, Zhang M-X, Liu Y, Su 10-L, Chen B, Zhang X-L. Peroxisome proliferator–activated receptor blastoff Expression changes in human pregnant myometrium. Reprod Sci. 2013 Jun;20(6):654–sixty. https://doi.org/ten.1177/1933719112461187.

    CAS  Article  PubMed  PubMed Key  Google Scholar

  56. Théry C, Witwer KW, Aikawa Eastward, Alcaraz MJ, Anderson JD, Andriantsitohaina R, et al. Minimal data for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. J Extracell Vesicles. 2018;seven(one):1535750. https://doi.org/10.1080/20013078.2018.1535750.

    Article  PubMed  PubMed Fundamental  Google Scholar

  57. Cakmak Genc G, Dursun A, Karakas Celik Due south, Calik M, Kokturk F, Piskin IE. IL28B, IL29 and micro-RNA 548 in subacute sclerosing panencephalitis as a rare disease. Cistron. 2018 Dec xv;678:73–8. https://doi.org/10.1016/j.gene.2018.07.062.

    CAS  Article  PubMed  Google Scholar

  58. Habieb A, Matboli M, El-Tayeb H, El-Asmar F. Potential function of lncRNA-TSIX, miR-548-a-3p, and SOGA1 mRNA in the diagnosis of hepatocellular carcinoma. Mol Biol Rep. 2019 Aug;46(4):4581–90. https://doi.org/10.1007/s11033-019-04810-x.

    CAS  Article  PubMed  Google Scholar

  59. Weber JA, Baxter DH, Zhang South, Huang DY, Huang KH, Lee MJ, et al. The MicroRNA Spectrum in 12 body fluids. Clin Chem. 2010 Nov;56(11):1733–41. https://doi.org/10.1373/clinchem.2010.147405.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  60. Abode - Cistron - NCBI [Internet]. [cited 2021 Jan 8]. Available from: https://www.ncbi.nlm.nih.gov/gene/?term=.

  61. Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, et al. Ensembl 2020. Nucleic Acids Res. 2020 Jan eight;48(D1):D682–eight. https://doi.org/10.1093/nar/gkz966.

    CAS  Article  PubMed  Google Scholar

  62. Waterhouse AM, Procter JB, Martin DMA, Clench M, Barton GJ. Jalview version two—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009 May ane;25(nine):1189–91. https://doi.org/10.1093/bioinformatics/btp033.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  63. Sievers F, Higgins DG. Clustal omega. Curr Protoc Bioinformatics. 2014 Dec 12;48(ane):3.13.1–16. https://doi.org/10.1002/0471250953.bi0313s48.

    Article  Google Scholar

  64. Saitou Due north, Nei 1000. The neighbor-joining method: a new method for reconstructing phylogenetic copse. Mol Biol Evol. 1987 Jul 1;4(4):406–25. https://doi.org/10.1093/oxfordjournals.molbev.a040454.

    CAS  Article  PubMed  PubMed Central  Google Scholar

  65. Bolger AM, Lohse Grand, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug one;thirty(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.

    CAS  Article  PubMed  PubMed Cardinal  Google Scholar

  66. Friedländer MR, Mackowiak SD, Li N, Chen Westward, Rajewsky Due north. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res. 2012 Jan;40(1):37–52. https://doi.org/10.1093/nar/gkr688.

    CAS  Article  PubMed  Google Scholar

  67. Robinson Doctor, McCarthy DJ, Smyth GK. edgeR: a Bioconductor packet for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan i;26(1):139–forty. https://doi.org/x.1093/bioinformatics/btp616.

    CAS  Article  PubMed  Google Scholar

  68. Metsalu T, Vilo J. ClustVis: a web tool for visualizing clustering of multivariate data using chief component analysis and heatmap. Nucleic Acids Res. 2015 Jul 1;43(W1):W566–lxx. https://doi.org/10.1093/nar/gkv468.

    CAS  Commodity  PubMed  PubMed Central  Google Scholar

Download references

Acknowledgments

Non applicable.

Funding

This work was financially supported by grants from the Enterprise Estonia (grant EU48695); Estonian Research Quango grants PSG433, PRG1076 and PSG608; Horizon 2020 innovation (ERIN) (grant no. EU952516) of the European Committee and by the Tallinn University of Technology development program 2016–2022, project code 2014–2020.four.01.sixteen–0032. The funding bodies played no role in the pattern of the report and collection, analysis, and interpretation of data and in writing the manuscript.

Author information

Affiliations

  1. Department of Chemical science and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia

    Ilmatar Rooda, Birgitta Kaselt, Maria Liivrand, Olli-Pekka Smolander & Agne Velthut-Meikas

  2. Competence Heart on Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia

    Ilmatar Rooda & Andres Salumets

  3. Division of Obstetrics and Gynecology, Department of Clinical Scientific discipline, Intervention and Technology (CLINTEC), Karolinska Institutet, 14186, Stockholm, Sweden

    Andres Salumets

  4. Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Fifty. Puusepa St. 8, 50406, Tartu, Estonia

    Andres Salumets

  5. Found of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia

    Andres Salumets

Contributions

IR, ML, OPS, AS, and AVM contributed to the study design; IR, BK and AVM analyzed the data. All authors were involved in compiling the manuscript and approved the final version.

Corresponding author

Correspondence to Ilmatar Rooda.

Ideals declarations

Ethics approving and consent to participate

Non applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that the research was conducted in the absence of whatever commercial or fiscal relationships that could be construed as a potential disharmonize of interest.

Additional data

Publisher'south Notation

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Data

Additional file ane: Supplementary Table S1.

Human hsa-mir-548 family pre-miRNA sequence locations in man genome. Supplementary Table S2. Hsa-mir-548 family miRNAs expressed in reproductive tissues. Supplementary Tabular array S3. Reactome pathways of predicted miRNA targets

Boosted file 2: Supplementary Fig. S1.

Phylogenetic tree of mature sequences of hsa-mir-548 family members. Supplementary Fig. S2. Phylogenetic tree of pre-miRNA sequences of miR-548 family unit members. Supplementary Fig. S3. Phylogenetic tree of Made1 and hsa-mir-548 family unit members. Supplementary Fig. S4. The alignment of Made1 and hsa-mir-548 family mature sequences

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original writer(due south) and the source, provide a link to the Creative Commons licence, and indicate if changes were fabricated. The images or other third party material in this commodity are included in the article's Artistic Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted utilize, y'all will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/nix/ane.0/) applies to the data made available in this commodity, unless otherwise stated in a credit line to the information.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Rooda, I., Kaselt, B., Liivrand, M. et al. Hsa-mir-548 family expression in man reproductive tissues. BMC Genom Data 22, 40 (2021). https://doi.org/x.1186/s12863-021-00997-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI : https://doi.org/10.1186/s12863-021-00997-w

Keywords

  • Hsa-mir-548 family unit
  • Hsa-miR-548ba
  • Granulosa cells
  • Myometrium, FSHR

houkancingingen.blogspot.com

Source: https://bmcgenomdata.biomedcentral.com/articles/10.1186/s12863-021-00997-w

0 Response to "The Role of Mirnas in Male Human Reproduction a Systematic Review"

Post a Comment

Subscribe to: Post Comments (Atom)

Iklan Atas Artikel

Iklan Tengah Artikel 1

Iklan Tengah Artikel 2

Iklan Bawah Artikel